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Re: [O] Bug? R: Org babel block execution *drastically* slower than in E
From: |
Thomas S. Dye |
Subject: |
Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly |
Date: |
Wed, 31 Oct 2012 10:56:16 -1000 |
Hi John,
Have you tried wrapping your R read in system.time()? If you are right
about :results silent eating up lots of time, then this should fix the
problem. system.time yields just a bit of output, so shouldn't slow
things down if writing out the data is indeed the problem as you
suspect.
hth,
Tom
John Hendy <address@hidden> writes:
> On Wed, Oct 31, 2012 at 3:12 PM, <address@hidden> wrote:
>
>> John Hendy <address@hidden> writes:
>>
>> > On Wed, Oct 31, 2012 at 11:41 AM, <span dir="ltr"><mailto:
>> address@hidden></span> wrote:
>> > John Hendy <mailto:address@hidden> writes:
>> >
>> >> I edited the subject to be more concise/clear.I let orgmode chug away
>> >> on reading in some ~10-30mb csv files for nearly 30min.
>> >
>> > [rest deleted]
>> >
>> > You need an ECM.I did my best to provide one, other than the file, which
>> I offered to provide if others requested that I upload it somewhere. Since
>> you have done so, so have I:
>> > - https://docs.google.com/open?id=0BzQupOSnvw08WHdabHh5VVczRGM
>>
>> > Let me know if that doesn't work. I put it on Google docs and
>> sometimes have issues with the sharing settings...
>>
>> Not an ECM in my book, but ...
>>
>>
> What else would you like? I provided:
> - the config
> - the data
> - how to [attempt to] reproduce
> - the org-mode text
>
>
>
>> On my 4 year old MacBook:
>>
>> ,----
>> |
>> | #+PROPERTY: session *R*
>> |
>> | #+name: bigcsv
>> | #+begin_src R
>> | bigcsv <- Sys.glob("~/Downloads/*.csv")
>> | #+end_src
>> |
>> | #+RESULTS: bigcsv
>> | : /Users/cberry/Downloads/test-file.csv
>> |
>> | #+name: readbig
>> | #+begin_src R :results output
>> | system.time(
>> | tmp <- read.csv(bigcsv)
>> | )
>> |
>> | #+end_src
>> |
>> | #+RESULTS: readbig
>> | : user system elapsed
>> | : 5.679 0.306 6.002
>> |
>> `----
>>
>> About the same as running from ESS.
>>
>>
> Not sure what to say. Looking for ways to troubleshoot or confirm. Since
> you can't confirm, any suggestions on where I should look for my issue? I
> can't explain it! All I know is that org chugs and chugs and the direct
> execution in ESS session is lightning fast.
>
>
>
> FYI,
>>
>> > dim(tmp)
>> [1] 964805 9
>>
>>
>>
> Was that just to show the size, or is something wrong with my file?
>
>
>> Chuck
>>
>>
>
> Thanks for attempting to replicate!
> John
>
>
>> [ rest deleted ]
>>
>>
>>
>>
> On Wed, Oct 31, 2012 at 3:12 PM, <address@hidden> wrote:
>
> John Hendy <address@hidden> writes:
>
> > On Wed, Oct 31, 2012 at 11:41 AM, <span
> dir="ltr"><mailto:address@hidden></span> wrote:
> > John Hendy <mailto:address@hidden> writes:
> >
> >> I edited the subject to be more concise/clear.I let orgmode
> chug away
> >> on reading in some ~10-30mb csv files for nearly 30min.
> >
> > [rest deleted]
> >
> > You need an ECM.I did my best to provide one, other than the
> file, which I offered to provide if others requested that I upload
> it somewhere. Since you have done so, so have I:
> > - https://docs.google.com/open?id=0BzQupOSnvw08WHdabHh5VVczRGM
>
> > Let me know if that doesn't work. I put it on Google docs
> and sometimes have issues with the sharing settings...
>
> Not an ECM in my book, but ...
>
>
>
> What else would you like? I provided:
> - the config
> - the data
> - how to [attempt to] reproduce
> - the org-mode text
>
>
>
> On my 4 year old MacBook:
>
> ,----
> |
> | #+PROPERTY: session *R*
> |
> | #+name: bigcsv
> | #+begin_src R
> | bigcsv <- Sys.glob("~/Downloads/*.csv")
> | #+end_src
> |
> | #+RESULTS: bigcsv
> | : /Users/cberry/Downloads/test-file.csv
> |
> | #+name: readbig
> | #+begin_src R :results output
> | system.time(
> | tmp <- read.csv(bigcsv)
> | )
> |
> | #+end_src
> |
> | #+RESULTS: readbig
> | : user system elapsed
> | : 5.679 0.306 6.002
> |
> `----
>
> About the same as running from ESS.
>
>
>
> Not sure what to say. Looking for ways to troubleshoot or confirm.
> Since you can't confirm, any suggestions on where I should look for my
> issue? I can't explain it! All I know is that org chugs and chugs and
> the direct execution in ESS session is lightning fast.
>
>
>
> FYI,
>
> > dim(tmp)
> [1] 964805 9
>
>
>
>
> Was that just to show the size, or is something wrong with my file?
>
>
> Chuck
>
>
>
>
> Thanks for attempting to replicate!
> John
>
>
> [ rest deleted ]
>
>
>
>
>
--
Thomas S. Dye
http://www.tsdye.com